Non-typhoidal Salmonella causing urinary tract infection in a young male with renal calculi – a case report and comprehensive review

Introduction. Non-typhoidal Salmonella (NTS) causes urinary tract infections infrequently and are usually associated with presence of genitourinary abnormalities. Case presentation. We report a case of immunocompetent male in his early 20 s with phimosis presented with history of dysuria and burning micturition for 4 months. A renal ultrasonography showed presence of bilateral intrarenal calculi. Urine analysis revealed presence of non-typhoidal Salmonella. Automated identification systems performed poorly in identification of serotype. On serotyping, it was identified as Salmonella enteritidis in the referral centre. The patient was managed with oral antibiotics. Conclusion. This report highlights the issues of inaccurate identification of NTS even with advanced automated systems and early initiation of therapy based on the knowledge of local susceptibility patterns. UTI in immunocompetent individuals by non-typhoidal Salmonella should always be investigated further to rule out genitourinary abnormalities and appropriate antibiotics must be started to avoid chronicity and complications.


INTRODUCTION
Salmonella is associated with various infections in humans, which includes typhoidal illness and non-typhoidal salmonellosis (NTS) [1].Non-typhoidal salmonellosis is a disease of great public health importance.Urinary tract infection due to NTS occurs infrequently and is observed predominantly in elderly patients with underlying diseases, diabetes mellitus, urologic abnormalities and immunosuppression.Modes of infection includes hematogenous spread from gastroenteritis and through direct urethral invasion especially in women [2].Salmonella enteritidis is the most frequently isolated Salmonella species in Europe and the USA [3].Because of absence of an effective nationwide surveillance system, NTS disease burden has been underestimated in India [1].Here, we present a case of young male with phimosis, renal calculi and chronic urinary tract infection due to non-typhoidal Salmonella after obtaining appropriate ethical approval.

CASE PRESENTATION
An unmarried male in his early 20s presented to the outpatient department (OPD) with complaints of dysuria and burning sensation during micturition for the past 4 months.He also had a history of nocturia (2-3 times).He denied history of fever, abdominal pain, increased frequency or urgency of urination, vomiting, hematuria and urethral discharge.This patient has received a course of intravenous antibiotic administration for treatment of UTI in another medical facility and documented evidence of therapy was not available with the patient.He did not have any co-morbidities like diabetes, hypertension or any other past chronic illness.He was a non-smoker and non-alcoholic.Urological history for voiding and storage symptoms was elicited.Apart from presenting symptoms, he did not have any complaints of incomplete voiding, increased intermittency, straining during voiding or urgency incontinence.He did not have any previous history of surgery.He was not on any medications.
On physical examination, he was conscious, oriented and had a normal build.There was no evidence of pallor, icterus, cyanosis, clubbing, lymphadenopathy or pedal oedema.Pulse rate was 88 beats per minute and blood pressure was 116/64 mm Hg.Respiratory rate was normal and auscultation revealed normal breath sounds present.On palpation, abdomen was soft without any tenderness or organomegaly and on auscultation, normal bowel sounds were heard.Physical examination of the cardiovascular and central nervous systems was unremarkable.Examination of genitourinary system revealed presence of congenital phimosis.There was no costovertebral angle tenderness.Digital rectal examination was normal.

Diagnostic assessments
The patient was advised to undergo ultrasonography (USG) of urinary system and specific laboratory investigations were done.An ultrasonography of urinary system showed right kidney measures 9.9×4.5 cm, normal in size and shows normal parenchymal echoes.Cortico medullary differentiation was present.Pelvicalyceal system and ureter were minimally dilated.Presence of multiple calculi was noticed in all the calyces, largest measuring 9 mm in the lower calyx of right kidney.Left kidney measures 10.6×5.6 cm, normal in size and showed normal parenchymal echoes and cortico medullary differentiation was present.Pelvicalyceal system and ureter were dilated with a calculus in the upper ureter measuring 9 mm.Also a calculus measuring 9 mm was noted in the middle calyx.No free fluid was seen in abdomen.Para aortic region and urinary bladder appeared normal.Prostate appeared normal in size and echoes.
Impression of bilateral intrarenal calculi with right minimal hydroureteronephrosis and left hydroureteronephrosis due to upper ureteric calculus was made.
Serum creatinine and random blood sugar were normal, 0.92 mg dl −1 and 123 mg dl −1 respectively.Glycosilated HbA1C was 5.4 %.Complete hemogram showed red cell count, total leucocyte count and platelet counts were within normal limits.
Urinalysis revealed macroscopic parameters within normal limits.Microscopy revealed increased WBCs (38 cells per high power field) and chemical analysis also showed the presence of leucocytes (3+), indication of UTI.Sample was negative for crystals or casts.
A clean catch midstream urine sample was sent to the microbiology department for aerobic culture and antimicrobial susceptibility testing.Wet mount microscopic examination showed 3-4 pus cells / hpf and presence of bacteria.
Semiquantitiative culture on urochrome agar showed colourless colonies greater than 10 5 colony forming units per millilitre and Gram-negative bacilli were seen on Gram-stain performed from the colony.Conventional biochemical tests led to presumptive identification of Salmonella spp.Biochemical reactions were as follows: Indole -negative, glucose fermented with gas production, lactose and sucrose not fermented, citrate utilised, urease -negative, mannitol motility mediumfermented and motile, triple sugar iron medium -K/A with gas and H 2 S, phenylpyruvic acid test -negative.Serotyping was performed with the antisera procured from Central Research Institute [CRI], Kasauli, India.The isolate was agglutinating with group specific O9 antisera but not with Hd.Denoting that it belonged to O9 group by Kauffman white Classification scheme.The isolate was found susceptible to ampicillin, ceftriaxone, ceftazidime, ciprofloxacin, azithromycin, chloramphenicol and cotrimoxazole by Kirby-Bauer disc diffusion method (CLSI).The isolate was identified as Salmonella enterica Group B or Group D with 98 % probability using Vitek two automated identification system (bioMérieux SA, France).The isolate was also subjected to MALDI-TOF Biotyper (Bruker Daltonik GmbH, Bremen, Germany) and was identified as Salmonella cholerasuis with a score value of 2.33, indicating highly probable species identification.This isolate was further sent to the National Salmonella and Escherichia Centre (NSEC), National Reference Centre for serotyping of Salmonella and Escherichia coli, CRI Kasauli, India and it was identified as Salmonella enteritidis (antigenic structure -9,12;gm:-) using serovar typing method.

Therapeutic interventions
The patient was started on T.ciprofloxacin 500 mg twice daily (BD) for 14 days for the treatment of UTI.He was also advised surgery (bilateral ureterorenoscopy [URS] with laser lithotripsy with bilateral Double J [DJ] stenting) for renal calculi and circumcision was advised for phimosis.

Follow-up and outcome
On telephonic reminder post-two weeks of his visit to OPD, for a review visit, he informed that his symptoms had resolved.Unfortunately the patient was lost to follow up and surgery could not be performed at our centre.

DISCUSSION
Salmonella enteritidis is emerging as a major cause of food-borne diseases and usually is associated with chicken eggs [4,5].Though extra-gastrointestinal tract focal infection has been mentioned, UTI due to NTS is uncommon.Worldwide, the overall incidence of NTS positive urine cultures has been estimated to be between 0.015 and 0.118% and about 18 % of these patients become chronic urinary carriers [6].In India, Salmonella enteritidis along with Salmonella typhimurium have been reported to be amongst the most common causes of human salmonellosis, which were found to account for 57-67 % of the total Salmonella isolates which were obtained from various human samples (includes blood, pus, faeces, urine and tissue) [1,4].NTS UTI is a surrogate marker of underlying predisposing factors such as unrecognized immune system suppression or anatomical abnormalities of genitourinary tract [2].Eng et al. published a case report along with a literature review of published reports containing data from 29 patients with UTI and NTS before the year 1987.Six cases out of 29 were found to be with urological abnormalities [7].In a comprehensive literature review published by Cohen et al., the authors reported 41/54 cases were carrying NTS where 18 cases were having urological abnormalities including renal calculi [8].In a retrospective analysis study published in 1996, Ramos et al. showed out of 28 cases with bacteriuria 24 patients were found to be infected with Salmonella enteritidis.Fourteen out of 28 patients were found to be with urological abnormalities [9].In a case reports study describing the retrospective analysis of 19 cases with UTI and NTS in University Hospital of Guadalajara, Spain, it has been shown that chronic diseases were found in 14 patients, eight patients had urolological abnormalities and S. enteritidis was the most common pathogen detected in 16 cases [10].It has been shown that Salmonella enterica serovar Typhi has the ability to form biofilms on the surface of human gall stones, likewise, NTS might colonize in the urinary tract system and form biofilms [11].
UTI leads to the formation of kidney stones where bacteria are responsible for the formation of renal calculi through urease enzymes.In a 2012, prospective study conducted by Tavichakorntrakool et al., the authors have shown that the bacterial cultures isolated from renal calculi from 100 stone former patients remained the same in both the core and the peripheral parts of the calculi.Renal calculi were associated with salmonella infection in only one patient of all the cases analysed [12].Salmonella enteritidis infection of the urinary tract is an uncommon condition.In phimosis condition, bacterial colonization occurring in the inner region of prepuce could lead to the establishment of urinary infections and circumcision plays an important role in minimising the risk of UTI [13].Results from non-randomized studies showed febrile UTI has been decreased in circumcised males compared to non-circumcised group [14].A meta analysis study published in 2005, included one randomized controlled trial, four cohort studies and seven case-control studies for the analysis with results showing the beneficial effect of circumcision in males who have a high risk of UTI.It should be noted that, the prevalence of circumcised males in countries like India, China, Japan and Taiwan is less than 20 % [15].Recently, it has been shown that boys with retractable prepuce had a lower risk of UTI when compared to cases with high grade phimosis and non-retractable foreskin.Boys with high grade phimosis (4-5) were prone to develop UTI when compared to the cases with lower grade phimosis (0-3) [16].In this study, our patient had phimosis, this further emphasizes that a thorough clinical examination of the genitourinary system is mandatory especially when the predisposition to chronic UTI is unlikely.
From literature review, it is understood that the pathogenesis of UTI by NTS is either by direct urethral invasion or by hematogenous spread in patients with previous episodes of gastroenteritis [2,17].Our patient did not have any previous history of gastroenteritis.Rodrigues et al. reported 85 % of patients with Salmonella cystitis had concurrent diarrhoea, whereas all patients with Salmonella pyelonephritis had concurrent bacteraemia in their study [18].Most recent case series report patients with only urinary tract symptoms and Salmonella isolated in urine culture but negative stool cultures for Salmonella species [19].
Salmonella serotype groups C1 and E were more commonly associated with UTIs in a study including 799 isolates of NTs from urine samples, in contrast to group D Salmonella UTI, as described in our case [20].Identification of NTS requires antisera to various serovars which is usually done at reference centres.More widely available systems for rapid identification of organisms like MALDI-TOF provides high accuracy in identification of Salmonella at species level but is limited to type or subtype Salmonella serovars [21,22].
NTS urine infection may be difficult to treat and early institution of antibiotics is associated with a favourable outcome.Complications due to Salmonella UTI warrants prolonged treatment, even though recurrences may still be seen [2].
Multidrug resistance (MDR) is not uncommon among NTS and it was observed in 75 % of NTS isolates in Sub-Saharan Africa.The number of ceftriaxone-resistant bloodstream isolates was seen to be 5 % between 2003 and 2013 in the USA [23].Resistance to ciprofloxacin was noticed as 8.9 % among NTS isolated from eggs.Also high prevalence of multiple antimicrobial resistance among NTS strains in a study in south India suggests possible prior selection by use of antimicrobials in egg production [24].Thus, sound judgement in antimicrobial use in both humans and food-producing animals is paramount to limit the spread of antibiotic resistance and the emergence of more virulent strains of Salmonella [23].Though this case report emphasizes thorough genitourinary examination in cases of chronic UTI and prior knowledge of prevalent NTS strains in the given locality, the main limitation of the study is the causal relationship between phimosis, renal calculi, and UTI.Renal calculi are more commonly associated with the development of chronic UTI by other well-known UTI-causing pathogens and rarely with NTS.Another limitation is the need to follow up with the patient for further interventions.
To summarize, Salmonella enteritidis is one of the infrequent pathogens causing chronic urinary tract infection and its detection is a challenge in resource limited settings due to inaccessibility to antisera.Automated identification systems have limitations in detection of Salmonellae serotypes.As multidrug resistance among NTS is rising due to inappropriate antibiotic usage in both human and animal industries, the knowledge of prevalence of MDR in local to geographic area is a must before starting therapy.

Author response to reviewers to Version 3
Dear Editor, Thank you very much for the comments and giving me the opportunity to revise my manuscript before proceeding to peer review.Please consider the following answers for the comments raised.
-Use of italics in the "et al" contractions in citations and bacterial genera and species names (e.g.Salmonella).Please correct this throughout the text.
Thank you for pointing out the font.Et al has been changed to "et al"through out (11 replacements made) -L56-58: "Urinary tract infection due to NTS infrequently, is predominantly observed in elderly patients with underlying diseases, diabetes mellitus, urologic abnormalities and immunosuppression."This sentence reads incomplete, please reword.
Sentence has been reframed.
-L152: "non typhoidal 'Salmonalla'" can be abbreviated to NTS throughout the text once the this acronym has been defined.Abbreviated to NTS -L155: change "be one of the most" to "be among the most" -changed -L158: "urinary infection", do you mean "urinary tract infection"?In that case it can be abbreviated to UTI as in other references to this term in the text Has been changed to NTS UTI.
-L191,193: Would "male" be a more appropriate terminology than "boy"?I have corrected in line 188 and 191 to males.However reference 15 and 16 has mentioned the study group as boys in their articles.Hence , corrections were not made for lines quoted from reference 16.

VERSION 3
Editor recommendation and comments https://doi.org/10.1099/acmi.0.000610.v3.1 © 2023 de Dios R.This is an open access peer review report distributed under the terms of the Creative Commons Attribution License.
Rubén de Dios; Brunel University London, Life Sciences, UNITED KINGDOM Date report received: 12 November 2023 Recommendation: Minor Amendment Comments: Thank you very much for submitting this revised manuscript to Access Microbiology and addressing the reviewer suggestions.I would like to commend your efforts for improving this report.However, the text still needs some minor amendments prior to acceptance.These include: -Use of italics in the "et al" contractions in citations and bacterial genera and species names (e.g.Salmonella).Please correct this throughout the text.-L56-58: "Urinary tract infection due to NTS infrequently, is predominantly observed in elderly patients with underlying diseases, diabetes mellitus, urologic abnormalities and immunosuppression."This sentence reads incomplete, please reword.-L152: "non typhoidal 'Salmonalla'" can be abbreviated to NTS throughout the text once the this acronym has been defined.-L155: change "be one of the most" to "be among the most" -L158: "urinary infection", do you mean "urinary tract infection"?In that case it can be abbreviated to UTI as in other references to this term in the text -L191,193: Would "male" be a more appropriate terminology than "boy"?

Author response to reviewers to Version 2
Dear Editor, Thank you very much for the your comments and giving me the opportunity to revise my manuscript before proceeding to peer review.Please consider the following answers for the queries raised.

Editor comments:
In this manuscript, Sriramajayam et al. describe a Salmonella urinary tract infection and its relationship with renal calculi and phimosis.The case is well described and the text can be easily followed.The manuscript has now been reviewed by two experts in the field, who have raised several issues and suggested multiple changes to the manuscript.Please take these comments into account carefully, especially those concerning: • The perspective to describe the novelty of the case, including the proposed amendments to the title • Discussing the renal calculi as a risk factor and the limitations in the diagnosis • Discussing the methods for Salmonella typing and their applicability As an additional suggestion, please provide a comprehensive literature review on the subject to better understand the case and its novelty.
Reply -Necessary changes have been made in the discussion section, taking all the points raised by the reviewers into consideration.

Reviewers' comments and responses to custom questions:
Please rate the quality of the presentation and structure of the manuscript We noticed small slip-up when typing in the written form of this paper that we will enumerate below: Line 32, change " immunocompetant " to immunocompetent ; -changed Line 39, change " the issues inaccurate " to the issues of inaccurate; -changed Line 69, change " complains " to complaints (substantive); -changed Line 133, change " his symptoms has resolved " to his symptoms had resolved ";-changed Line 145, change " include" to including (adjective); -changed Line 138, change " and usually is associated ", to is usually associated-changed Line 149, change " clinical examination of genitourinary " to clinical examination of the genitourinary; -changed Line 157,change "Salmonella isolated on urine" to Salmonella isolated in urine ; -changed Line 179, change "pathogen causing " to pathogens causing ";-changed Line 184 , change "geographic area is must before " to geographic area is a must before .Reviewer 2 Comments to Author: The case is well described and the results are clearly presented and coherent.However, the reviewer disagrees with the title as well as several points raised in the conclusion.
The phimosis is highly unlikely to have contributed in any way to the urinary tract infection (UTI).Unless the phimosis is extreme enough to inhibit urinary flow or voiding of the bladder, it is not a risk factor for UTI.Therefore phimosis should be omitted from the title.
Phimosis is deleted in the title and title is changed accordingly However, renal calculi are a well known factor predisposing to UTI, including with Salmonella (check MEDLINE with the keywords ).The case description is suggestive since the symptoms were present for several months before admission of the patient.The "absence" of gastroenteritis is therefore no surprise and the patient may well have failed to remember an episode of diarrhea shortly before onset of his urinary symptoms.Of notice, the infection tends to be chronic in the presence of urinary stones as shown in the case described.
Points mentioned in the discussion part.(line171-179) Identification of nontyphoidal Salmonella: this has been well done in the paper.Serotyping of Salmonella isolates in a reference laboratory is always mandatory for isolates from urine.
Identification with commerial biochemical tests will usually be reliable in excluding Salmonella ser.Typhi; MALDI is not suitable as a replacement for serotyping (as shown by your results: Samonella ser.Choleraesuis is definitely a misleading result of MALDI and the BRUKER database should not contain this host-specific serovar).However, there is no necessity for serotype identification and this should be omitted from the title.All Salmonella serovars are "equal" (with the exception of S. typhi and other host-adapted serovars of course) .
'necessity for serotype identification' omitted from the title.In the discussion section, the importance of identification has been elaborated as antimicrobial resistance is increasing among the NTS and a study from the same locality shows NTS resistant to few of the commonly used antibiotics.Hence proper identification can guide in choosing appropriate antimicrobial agents.
It is a pity that the patient was lost to follow-up because recurrence of Salmonella is possible if nephrolithiasis is not treated.

VERSION 2
Editor recommendation and comments https://doi.org/10.1099/acmi.0.000610.v2.3 © 2023 de Dios R.This is an open access peer review report distributed under the terms of the Creative Commons Attribution License.Comments: In this manuscript, Sriramajayam et al. describe a Salmonella urinary tract infection and its relationship with renal calculi and phimosis.The case is well described and the text can be easily followed.The manuscript has now been reviewed by two experts in the field, who have raised several issues and suggested multiple changes to the manuscript.Please take these comments into account carefully, especially those concerning: • The perspective to describe the novelty of the case, including the proposed amendments to the title • Discussing the renal calculi as a risk factor and the limitations in the diagnosis • Discussing the methods for Salmonella typing and their applicability As an additional suggestion, please provide a comprehensive literature review on the subject to better understand the case and its novelty.Please provide a revised version of the manuscript, as well as a point-by-point response to the reviewers' comments, within 2 months.Comments: The case is well described and the results are clearly presented and coherent.However, the reviewer disagrees with the title as well as several points raised in the conclusion.The phimosis is highly unlikely to have contributed in any way to the urinary tract infection (UTI).Unless the phimosis is extreme enough to inhibit urinary flow or voiding of the bladder, it is not a risk factor for UTI.Therefore phimosis should be omitted from the title.However, renal calculi are a well known factor predisposing to UTI, including with Salmonella (check MEDLINE with the keywords nephrolithiasis and Salmonella).The case description is suggestive since the symptoms were present for several months before admission of the patient.The "absence" of gastroenteritis is therefore no surprise and the patient may well have failed to remember an episode of diarrhea shortly before onset of his urinary symptoms.Of notice, the infection tends to be chronic in the presence of urinary stones as shown in the case described.Identification of nontyphoidal Salmonella: this has been well done in the paper.Serotyping of Salmonella isolates in a reference laboratory is always mandatory for isolates from urine.Identification with commerial biochemical tests will usually be reliable in excluding Salmonella ser.Typhi; MALDI is not suitable as a replacement for serotyping (as shown by your results: Samonella ser.Choleraesuis is definitely a misleading result of MALDI and the BRUKER database should not contain this host-specific serovar).However, there is no necessity for serotype identification and this should be omitted from the title.All Salmonella serovars are "equal" (with the exception of S. typhi and other host-adapted serovars of course) .It is a pity that the patient was lost to follow-up because recurrence of Salmonella is possible if nephrolithiasis is not treated.

Please rate the quality of the presentation and structure of the manuscript Satisfactory
To what extent are the conclusions supported by the data?Strongly support

If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines? Yes
Reviewer 1 recommendation and comments https://doi.org/10.1099/acmi.0.000610.v2.1 © 2023 Damasco P.This is an open access peer review report distributed under the terms of the Creative Commons Attribution License.
Paulo Damasco; Hospital Universitario Pedro Ernesto -UERJ, Departamento de Medicina Interna, Av. 28 de Setembro 87, 3o Andar -DIP, Brasil, Rio de Janeiro, BRAZIL Date report received: 28 June 2023 Recommendation: Minor Amendment Comments: This case report recalls the possibility that phimosis is a risk factor for non-typhoidal Salmonella urinary tract infection.We noticed small slip-up when typing in the written form of this paper that we will enumerate below: Line 32, change " immunocompetant " to immunocompetent ; Line 39, change " the issues inaccurate " to the issues of inaccurate; Line 69, change " complains " to complaints (substantive); Line 133, change " his symptoms has resolved " to his symptoms had resolved "; Line 145, change " include" to including (adjective); Line 138, change " and usually is associated ", to is usually associated Line 149, change " clinical examination of genitourinary " to clinical examination of the genitourinary; Line 157,change "Salmonella isolated on urine" to Salmonella isolated in urine ; Line 179, change "pathogen causing " to pathogens causing "; Line 184 , change "geographic area is must before " to geographic area is a must before .We need to change the introduction to Non-typhoidal salmonellosis (NTS) is a disease of great public health importance.Urinary tract infection due to NTS infrequently, is predominantly observed in elderly patients with underlying diseases, diabetes mellitus, urologic abnormalities and immunosuppression.It would be interesting to note in the text the limitation of this report case of urinary tract infection due to NTS.

Please rate the quality of the presentation and structure of the manuscript Satisfactory
To what extent are the conclusions supported by the data?Strongly support

Author response to reviewers to Version 1
Dear Editor, Thank you very much for the your comments and giving me the opportunity to revise my manuscript before proceeding to peer review.Please consider the following answers for the queries raised.
• There is a Table 1 cited in L108 and L114 which does not appear in the section dedicated to contain figures and tables (L131).I had removed the table before submission, considering complete elaboration of biochemical reactions can be done in text.And I overlooked to remove the annotation from manuscript."Table1' has been removed from the script.
Biochemical reactions had been added in the manuscript.L 108 to 111.
• Bacterial species names need to be in italics.
The font of bacterial species has been changed to italics where ever it appears in manuscript.
• It is stated that this is the first case report on salmonellosis in an adult with phimosis (L57-59).However, L79 mentions phimosis is a congenital condition, which makes it coincidental to occur with Salmonella UTI rather than being directly related, as it is conveyed by the report.Similarly, the renal calculi found in the patient do not seem to show any relation with the infection as the manuscript reads.Additionally, Yeung (2021, 10.3390/idr13010023) already mentions (without detailed description) a patient with phimosis presenting a Salmonella enteritidis infection, but it is not mentioned in the references.Sir, while doing pubmed search with MeSH words (phimosis) AND (salmonella), there were no case reports found.Hence, we did not include it in the references.The study done by Yeung proves that urological procedure can be a possible risk factor for Salmonella bacteraemia and one specific case has undergone dorsal slit procedure for phimosis and had developed Salmonella bacteraemia.Hence, we have updated our discussion section with a reference to the article by Yeung (2021, 10.3390/idr13010023).L 154-156.
We also agree that phimosis is congenital condition.This case report is to emphasis that non typhoidal salmonella UTI is more common with genitourinary abnormalities similar to previously published case reports.
• There are multiple abbreviations without definition (e.g., BD, URS, DJ, OPD…) The abbreviations are expanded in the manuscript as twice daily (BD), Ureterorenoscope (URS), Double J stent (DJ) Outpatient Department (OPD) • The highlight of the case report is the issues in identifying and serotyping the Salmonella isolate.However, the descriptions of these (L110-120) do not reflect that hindrance and arelacking some more elaboration and context to comprehensively address this problematic.Later on, the Discussion section does not elaborate on it either.
The highlight of the case report is difficulty in identifying the serotype of Salmonella, as in low and lower middle income countries, the primary method of identification is by biochemical reactions and in some corporate diagnostic centers, automated system like VITEK 2 is used.Availability of antisera for serotyping is very limited and majority of the hospitals do not have antisera for diagnostic purposes.We also mention that automated systems performed poorly in identification of the serotype of Salmonella though the confidence level of these systems for identification has been very high.
We were able to identify the isolate as NTS, but further serotyping could not be performed in our centre due to limited availability of antisera.Automated systems also did not perform well in identification of the serotype.Hence we had to send the isolate to the referral centre for identification and it took few days before the final report was received.
One more line has been added highlighting the limitation of MALDI TOF MS in poor identification of serotypes.L 163-165.
Second thing we wanted to point out that knowledge of antimicrobial susceptibility of the non typhoid salmonella prevalent in a particular geographical location is also important.
• In the Discussion section, there is a paragraph dedicated to AMR issues with Salmonella isolates (L165-172).However, the case does not present any issue related to this, which makes it hard to reconcile this paragraph with the rest of the manuscript.
Though our isolate was sensitive to all the drugs used for UTI, we would like to throw light on the prevalence of drug resistance among NTS isolates.The study by Suresh T et al conducted in our location on eggs and egg trays showed all the NTS isolates were resistant to ampicillin, neomycin, polymyxin-B and tetracycline.

L172-173 added.
As the patients with UTI are started on empirical antibiotics under syndromic approach even before the culture reports are available.Also the frequency of patients who are lost to follow up is quite high, a good knowledge about local antimicrobial resistance pattern will help guide in choosing the right antibiotic.
There are multiple sentences that are hard to understand as they read.This would require a revision of the writing to make them more readable.Specific examples are: The quoted sentences were rephrased as follows: o L50-51: "Hematogenous spread from gastroenteritis and in women, more commonly through direct urethral invasion has been observed as modes of infection".
Changed to "Modes of infection includes hematogenous spread from gastroenteritis and through direct urethral invasion especially in women" o L65-67: "He gave history of intravenous antibiotic administration for his symptoms of UTI in another medical facility and details of which were not available with the patient".
Changed to "This patient has received a course of intravenous antibiotic administration for treatment of UTI in another medical facility and documented evidence of therapy was not available with the patient." o L67-68: "No history of any co morbidities like diabetes, hypertension or any other chronic illness".
Changed to "He did not have any co-morbidities like diabetes, hypertension or any other past chronic illness" o L76-77: "Abdomen was soft and non-tender without any organomegaly and on palpation and normal bowel sounds were heard".
Changed to "On palpation, the abdomen was soft without any tenderness or organomegaly and on auscultation, normal bowel sounds were heard" o L110-112: "Automated identification revealed the identification as Salmonella enterica Group B or Group D (98% probability) with excellent identification confidence using Vitek 2 automated identification system (bioMerieux SA, France)".
Changed to "The isolate was identified as Salmonella enterica Group B or Group D with 98% probability using Vitek 2 automated identification system (bioMérieux SA, France)" o L144-147: "Our patient had phimosis, this further emphasizes that a thorough clinical examination of genitourinary system is mandatory especially when the predisposition to chronic UTI is unlikely such as our patient who is an immunocompetent young male".Changed to "Our patient had phimosis, this further emphasizes that a thorough clinical examination of genitourinary system is mandatory especially when the predisposition to chronic UTI is unlikely" o L176: "…hence strong suspicion is the key".
The sentence was rephrased and the quote line has been removed.Comments: Dear Authors, Thank you very much for submitting this case report to Access Microbiology.However, although it presents interesting findings, several points need improvement before progressing to peer review.Please consider the following points for a revised version of the manuscript: • There is a Table 1 cited in L108 and L114 which does not appear in the section dedicated to contain figures and tables (L131).• Bacterial species names need to be in italics.• It is stated that this is the first case report on salmonellosis in an adult with phimosis (L57-59).However, L79 mentions phimosis is a congenital condition, which makes it coincidental to occur with Salmonella UTI rather than being directly related, as it is conveyed by the report.Similarly, the renal calculi found in the patient do not seem to show any relation with the infection as the manuscript reads.Additionally, Yeung (2021, 10.3390/idr13010023) already mentions (without detailed description) a patient with phimosis presenting a Salmonella enteritidis infection, but it is not mentioned in the references.• There are multiple abbreviations without definition (e.g., BD, URS, DJ, OPD…) • The highlight of the case report is the issues in identifying and serotyping the Salmonella isolate.However, the descriptions of these (L110-120) do not reflect that hindrance and are lacking some more elaboration and context to comprehensively address this problematic.Later on, the Discussion section does not elaborate on it either.• In the Discussion section, there is a paragraph dedicated to AMR issues with Salmonella isolates (L165-172).However, the case does not present any issue related to this, which makes it hard to reconcile this paragraph with the rest of the manuscript.• There are multiple sentences that are hard to understand as they read.This would require a revision of the writing to make them more readable.Specific examples are: o L50-51: "Hematogenous spread from gastroenteritis and in women, more commonly through direct urethral invasion has been observed as modes of infection".o L65-67: "He gave history of intravenous antibiotic administration for his symptoms of UTI in another medical facility and details of which were not available with the patient".o L67-68: "No history of any co morbidities like diabetes, hypertension or any other chronic illness".o L76-77: "Abdomen was soft and non-tender without any organomegaly and on palpation and normal bowel sounds were heard".o L110-112: "Automated identification revealed the identification as Salmonella enterica Group B or Group D (98% probability) with excellent identification confidence using Vitek 2 automated identification system (bioMerieux SA, France)".o L144-147: "Our patient had phimosis, this further emphasizes that a thorough clinical examination of genitourinary system is mandatory especially when the predisposition to chronic UTI is unlikely such as our patient who is an immunocompetant young male".o L176: "…hence strong suspicion is the key".Please provide a revised version of this manuscript within 1 month together with a point-by-point response to these comments.Additional practical information on case report writing and good practice can be found in the CARE checklist (https:// www.care-statement.org/ checklist).Do not hesitate to contact me or the Access Microbiology Editorial Office if you need any assistance during the process.

VERSION 4 Editor
recommendation and comments https://doi.org/10.1099/acmi.0.000610.v4.1 © 2023 de Dios R.This is an open access peer review report distributed under the terms of the Creative Commons Attribution License.Rubén de Dios; Brunel University London, Life Sciences, UNITED KINGDOM Date report received: 17 November 2023 Recommendation: Accept Comments: Thank you very much for submitting your revised manuscript to Access Microbiology and address the suggested changes.I am pleased to inform you that this work is now accepted for publication.Congratulations to all authors!

Reviewer 1 :
SatisfactoryTo what extent are the conclusions supported by the data?Reviewer 1: Strongly support Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?Reviewer 1: No: If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?Reviewer 1: Yes: Reviewer 1 Comments to Author: This case report recalls the possibility that phimosis is a risk factor for non-typhoidal Salmonella urinary tract infection.
-changed We need to change the introduction to Non-typhoidal salmonellosis (NTS) is a disease of great public health importance.Urinary tract infection due to NTS infrequently, is predominantly observed in elderly patients with underlying diseases, diabetes mellitus, urologic abnormalities and immunosuppression.-has been added to the introduction It would be interesting to note in the text the limitation of this report case of urinary tract infection due to NTS. reply -all the grammatical errors and slip ups have been addressed.Limitations of the study has been added in the discussion section ( line 220 -225) Please rate the quality of the presentation and structure of the manuscript Reviewer 2: Satisfactory To what extent are the conclusions supported by the data?Reviewer 2: Strongly support Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?Reviewer 2: No: If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?Reviewer 2: Yes: Dios; Brunel University London, Life Sciences, UNITED KINGDOM Date report received: 03 July 2023 Recommendation: Major Revision